When hostage negotiators and FBI agents riding on a U.S. Coast Guard boat pulled alongside the stolen 40-foot sailing yacht captained by a man they believed had kidnapped his two children from South San Francisco, they were prepared for a fight.

But Christopher Maffei gave up without one, authorities said.

Maffei, 42, put his hands on his head and was arrested without incident after a three-day search that ended Friday evening in waters off the Monterey Peninsula, said South San Francisco police spokesman Bruce McPhillips.

“He didn’t have a whole lot of resistance in him left,” McPhillips said Saturday as he recounted details of the rescue.

Authorities say Maffei stole the yacht in Alameda and set sail with the children, ages 2 and 3, without their mother’s permission.

Coast Guard spokesman Thomas McKenzie said officials spotted the boat, christened “Unleashed,” about 10 a.m. Friday and watched it from afar all day. He said they waited to move in because they didn’t want to “spook him and send him out to sea.”

A 47-foot Coast Guard cutter, with FBI agents and hostage negotiators aboard, followed the stolen vessel for hours, with another Coast Guard boat nearby, before making contact with Maffei just after 8 p.m.

“They deployed a smaller boat, went up alongside the yacht, made contact with him, then provided him with water and a two-way radio,” McPhillips said. “At that point he expressed that he wanted to give up. They requested to board his boat, did so, rescued the kids and took him into custody without incident.”

The children were taken ashore and examined by medics and deemed to be in good health, McPhillips said. By Saturday morning, they were back at home in South San Francisco with their mother.

“Under the circumstances I’m sure they’re glad to be off the boat,” McPhillips said.

“The boat has been secured at a Coast Guard facility in Monterey and will be processed for evidence,” he said. “After that it will be returned to the owner.”

Maffei was being held on $200,000 bail Saturday at Maguire Correctional Facility in Redwood City, said San Mateo County sheriff’s spokesman Larry Schumaker. He was booked on charges that include kidnapping, violation of a custody decree, willful cruelty to children likely to cause injury or death and using force to take a child away from another person.

The case is under review by the San Mateo County District Attorney’s Office, and Maffei is set to be arraigned Monday at 1:30 p.m. in Redwood City at San Mateo County’s Hall of Justice, Schumaker said.

A restraining order request filed by Maffei’s estranged girlfriend, Jennifer Hipon, had a hearing date of Sept. 21. It requests no visitation rights for Maffei for their children, Brooklynn, 3, and Devin, 2.

Maffei had moved to Thailand in 2010, and Hipon feared he might snatch the kids and take them to Wyoming, Switzerland or Thailand.

Hipon said he nabbed the kids Tuesday by opening a sliding-glass door and hooking one under each arm before fleeing down the street.

Police said that Maffei had been to the Alameda harbor just two weeks before — with the children in tow — to speak with the owner of “Unleashed” about purchasing a boat.